1
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Robust total X-ray scattering workflow to study correlated motion of proteins in crystals. Nat Commun 2023; 14:1228. [PMID: 36869043 PMCID: PMC9984388 DOI: 10.1038/s41467-023-36734-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/15/2023] [Indexed: 03/05/2023] Open
Abstract
The breathing motions of proteins are thought to play a critical role in function. However, current techniques to study key collective motions are limited to spectroscopy and computation. We present a high-resolution experimental approach based on the total scattering from protein crystals at room temperature (TS/RT-MX) that captures both structure and collective motions. To reveal the scattering signal from protein motions, we present a general workflow that enables robust subtraction of lattice disorder. The workflow introduces two methods: GOODVIBES, a detailed and refinable lattice disorder model based on the rigid-body vibrations of a crystalline elastic network; and DISCOBALL, an independent method of validation that estimates the displacement covariance between proteins in the lattice in real space. Here, we demonstrate the robustness of this workflow and further demonstrate how it can be interfaced with MD simulations towards obtaining high-resolution insight into functionally important protein motions.
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2
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Klebl DP, Wang Y, Sobott F, Thompson RF, Muench SP. It started with a Cys: Spontaneous cysteine modification during cryo-EM grid preparation. Front Mol Biosci 2022; 9:945772. [PMID: 35992264 PMCID: PMC9389043 DOI: 10.3389/fmolb.2022.945772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/27/2022] [Indexed: 12/31/2022] Open
Abstract
Advances in single particle cryo-EM data collection and processing have seen a significant rise in its use. However, the influences of the environment generated through grid preparation, by for example interactions of proteins with the air-water interface are poorly understood and can be a major hurdle in structure determination by cryo-EM. Initial interactions of proteins with the air-water interface occur quickly and proteins can adopt preferred orientation or partially unfold within hundreds of milliseconds. It has also been shown previously that thin-film layers create hydroxyl radicals. To investigate the potential this might have in cryo-EM sample preparation, we studied two proteins, HSPD1, and beta-galactosidase, and show that cysteine residues are modified in a time-dependent manner. In the case of both HSPD1 and beta-galactosidase, this putative oxidation is linked to partial protein unfolding, as well as more subtle structural changes. We show these modifications can be alleviated through increasing the speed of grid preparation, the addition of DTT, or by sequestering away from the AWI using continuous support films. We speculate that the modification is oxidation by reactive oxygen species which are formed and act at the air-water interface. Finally, we show grid preparation on a millisecond timescale outruns cysteine modification, showing that the reaction timescale is in the range of 100s to 1,000s milliseconds and offering an alternative approach to prevent spontaneous cysteine modification and its consequences during cryo-EM grid preparation.
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Affiliation(s)
- David P. Klebl
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Yiheng Wang
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Frank Sobott
- School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Rebecca F. Thompson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
- *Correspondence: Rebecca F. Thompson, ; Stephen P. Muench,
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
- *Correspondence: Rebecca F. Thompson, ; Stephen P. Muench,
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3
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Mañas‐Torres MC, Illescas‐Lopez S, Gavira JA, de Cienfuegos LÁ, Marchesan S. Interactions Between Peptide Assemblies and Proteins for Medicine. Isr J Chem 2022. [DOI: 10.1002/ijch.202200018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mari C. Mañas‐Torres
- Departamento de Química Orgánica, Facultad de Ciencias Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ) Universidad de Granada, (UGR) C. U. Fuentenueva Avda. Severo Ochoa s/n E-18071 Granada
| | - Sara Illescas‐Lopez
- Departamento de Química Orgánica, Facultad de Ciencias Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ) Universidad de Granada, (UGR) C. U. Fuentenueva Avda. Severo Ochoa s/n E-18071 Granada
| | - José A. Gavira
- Laboratorio de Estudios Cristalográficos Instituto Andaluz de Ciencias de la Tierra (Consejo Superior de Investigaciones Científicas-UGR) Avenida de las Palmeras 4 18100 Armilla, UEQ Granada Spain
| | - Luis Álvarez de Cienfuegos
- Departamento de Química Orgánica, Facultad de Ciencias Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente (UEQ) Universidad de Granada, (UGR) C. U. Fuentenueva Avda. Severo Ochoa s/n E-18071 Granada
- Instituto de Investigación Biosanitaria ibs Granada Spain
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department University of Trieste Via L. Giorgieri 1 Trieste 34127 Italy
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4
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Stachowski TR, Snell ME, Snell EH. A SAXS-based approach to rationally evaluate radical scavengers - toward eliminating radiation damage in solution and crystallographic studies. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1309-1320. [PMID: 34475280 PMCID: PMC8415334 DOI: 10.1107/s1600577521004045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/15/2021] [Indexed: 05/30/2023]
Abstract
X-ray-based techniques are a powerful tool in structural biology but the radiation-induced chemistry that results can be detrimental and may mask an accurate structural understanding. In the crystallographic case, cryocooling has been employed as a successful mitigation strategy but also has its limitations including the trapping of non-biological structural states. Crystallographic and solution studies performed at physiological temperatures can reveal otherwise hidden but relevant conformations, but are limited by their increased susceptibility to radiation damage. In this case, chemical additives that scavenge the species generated by radiation can mitigate damage but are not always successful and the mechanisms are often unclear. Using a protein designed to undergo a large-scale structural change from breakage of a disulfide bond, radiation damage can be monitored with small-angle X-ray scattering. Using this, we have quantitatively evaluated how three scavengers commonly used in crystallographic experiments - sodium nitrate, cysteine, and ascorbic acid - perform in solution at 10°C. Sodium nitrate was the most effective scavenger and completely inhibited fragmentation of the disulfide bond at a lower concentration (500 µM) compared with cysteine (∼5 mM) while ascorbic acid performed best at 5 mM but could only reduce fragmentation by ∼75% after a total accumulated dose of 792 Gy. The relative effectiveness of each scavenger matches their reported affinities for solvated electrons. Saturating concentrations of each scavenger shifted fragmentation from first order to a zeroth-order process, perhaps indicating the direct contribution of photoabsorption. The SAXS-based method can detect damage at X-ray doses far lower than those accessible crystallographically, thereby providing a detailed picture of scavenger processes. The solution results are also in close agreement with what is known about scavenger performance and mechanism in a crystallographic setting and suggest that a link can be made between the damage phenomenon in the two scenarios. Therefore, our engineered approach might provide a platform for more systematic and comprehensive screening of radioprotectants that can directly inform mitigation strategies for both solution and crystallographic experiments, while also clarifying fundamental radiation damage mechanisms.
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Affiliation(s)
- Timothy R. Stachowski
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
- Cell Stress Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA
| | - Mary E. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, NY 14203, USA
- Materials Design and Innovation, State University at New York at Buffalo, 700 Ellicott St, Buffalo, NY 14203, USA
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5
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Jain R, Abel D, Rakitin M, Sullivan M, Lodowski DT, Chance MR, Farquhar ER. New high-throughput endstation to accelerate the experimental optimization pipeline for synchrotron X-ray footprinting. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1321-1332. [PMID: 34475281 PMCID: PMC8415340 DOI: 10.1107/s1600577521005026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/11/2021] [Indexed: 05/30/2023]
Abstract
Synchrotron X-ray footprinting (XF) is a growing structural biology technique that leverages radiation-induced chemical modifications via X-ray radiolysis of water to produce hydroxyl radicals that probe changes in macromolecular structure and dynamics in solution states of interest. The X-ray Footprinting of Biological Materials (XFP) beamline at the National Synchrotron Light Source II provides the structural biology community with access to instrumentation and expert support in the XF method, and is also a platform for development of new technological capabilities in this field. The design and implementation of a new high-throughput endstation device based around use of a 96-well PCR plate form factor and supporting diagnostic instrumentation for synchrotron XF is described. This development enables a pipeline for rapid comprehensive screening of the influence of sample chemistry on hydroxyl radical dose using a convenient fluorescent assay, illustrated here with a study of 26 organic compounds. The new high-throughput endstation device and sample evaluation pipeline now available at the XFP beamline provide the worldwide structural biology community with a robust resource for carrying out well optimized synchrotron XF studies of challenging biological systems with complex sample compositions.
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Affiliation(s)
- Rohit Jain
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Donald Abel
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Maksim Rakitin
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Michael Sullivan
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - David T. Lodowski
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Mark R. Chance
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Erik R. Farquhar
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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6
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Kuei B, Gomez ED. Pushing the limits of high-resolution polymer microscopy using antioxidants. Nat Commun 2021; 12:153. [PMID: 33420049 PMCID: PMC7794589 DOI: 10.1038/s41467-020-20363-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 11/26/2020] [Indexed: 01/29/2023] Open
Abstract
High-resolution transmission electron microscopy (HRTEM) has been transformative to the field of polymer science, enabling the direct imaging of molecular structures. Although some materials have remarkable stability under electron beams, most HRTEM studies are limited by the electron dose the sample can handle. Beam damage of conjugated polymers is not yet fully understood, but it has been suggested that the diffusion of secondary reacting species may play a role. As such, we examine the effect of the addition of antioxidants to a series of solution-processable conjugated polymers as an approach to mitigating beam damage. Characterizing the effects of beam damage by calculating critical dose DC values from the decay of electron diffraction peaks shows that beam damage of conjugated polymers in the TEM can be minimized by using antioxidants at room temperature, even if the antioxidant does not alter or incorporate into polymer crystals. As a consequence, the addition of antioxidants pushes the resolution limit of polymer microscopy, enabling imaging of a 3.6 Å lattice spacing in poly[(5,6-difluoro-2,1,3-benzothiadiazol-4,7-diyl)-alt-(3,3″'-di(2-octyldodecyl)-2,2';5',2″;5″,2″'-quaterthiophene-5,5″'-diyl)] (PffBT4T-2OD).
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Affiliation(s)
- Brooke Kuei
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Enrique D Gomez
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA.
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA.
- Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA.
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7
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Castellví A, Pascual-Izarra C, Crosas E, Malfois M, Juanhuix J. Improving data quality and expanding BioSAXS experiments to low-molecular-weight and low-concentration protein samples. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:971-981. [PMID: 33021499 DOI: 10.1107/s2059798320010700] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 08/03/2020] [Indexed: 11/10/2022]
Abstract
The addition of compounds to scavenge the radical species produced during biological small-angle X-ray scattering (BioSAXS) experiments is a common strategy to reduce the effects of radiation damage and produce better quality data. As almost half of the experiments leading to structures deposited in the SASBDB database used scavengers, finding potent scavengers would be advantageous for many experiments. Here, four compounds, three nucleosides and one nitrogenous base, are presented which can act as very effective radical-scavenging additives and increase the critical dose by up to 20 times without altering the stability or reducing the contrast of the tested protein solutions. The efficacy of these scavengers is higher than those commonly used in the field to date, as verified for lysozyme solutions at various concentrations from 7.0 to 0.5 mg ml-1. The compounds are also very efficient at mitigating radiation damage to four proteins with molecular weights ranging from 7 to 240 kDa and pH values from 3 to 8, with the extreme case being catalase at 6.7 mg ml-1, with a scavenging factor exceeding 100. These scavengers can therefore be instrumental in expanding BioSAXS to low-molecular-weight and low-concentration protein samples that were previously inaccessible owing to poor data quality. It is also demonstrated that an increase in the critical dose in standard BioSAXS experiments leads to an increment in the retrieved information, in particular at higher angles, and thus to higher resolution of the model.
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Affiliation(s)
- Albert Castellví
- Experiments Division, ALBA Synchrotron, Carrer de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Carlos Pascual-Izarra
- Experiments Division, ALBA Synchrotron, Carrer de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Eva Crosas
- DESY Photon Science, Notkestrasse 85, 08290 Hamburg, Germany
| | - Marc Malfois
- Experiments Division, ALBA Synchrotron, Carrer de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Judith Juanhuix
- Experiments Division, ALBA Synchrotron, Carrer de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
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8
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Efficacy of aldose reductase inhibitors is affected by oxidative stress induced under X-ray irradiation. Sci Rep 2019; 9:3177. [PMID: 30816220 PMCID: PMC6395642 DOI: 10.1038/s41598-019-39722-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/29/2019] [Indexed: 01/01/2023] Open
Abstract
Human aldose reductase (hAR, AKR1B1) has been explored as drug target since the 1980s for its implication in diabetic complications. An activated form of hAR was found in cells from diabetic patients, showing a reduced sensitivity to inhibitors in clinical trials, which may prevent its pharmacological use. Here we report the conversion of native hAR to its activated form by X-ray irradiation simulating oxidative stress conditions. Upon irradiation, the enzyme activity increases moderately and the potency of several hAR inhibitors decay before global protein radiation damage appears. The catalytic behavior of activated hAR is also reproduced as the KM increases dramatically while the kcat is not much affected. Consistently, the catalytic tetrad is not showing any modification. The only catalytically-relevant structural difference observed is the conversion of residue Cys298 to serine and alanine. A mechanism involving electron capture is suggested for the hAR activation. We propose that hAR inhibitors should not be designed against the native protein but against the activated form as obtained from X-ray irradiation. Furthermore, since the reactive species produced under irradiation conditions are the same as those produced under oxidative stress, the described irradiation method can be applied to other relevant proteins under oxidative stress environments.
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9
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Caterino M, Herrmann M, Merlino A, Riccardi C, Montesarchio D, Mroginski MA, Musumeci D, Ruffo F, Paduano L, Hildebrandt P, Kozuch J, Vergara A. On the pH-Modulated Ru-Based Prodrug Activation Mechanism. Inorg Chem 2019; 58:1216-1223. [PMID: 30614697 DOI: 10.1021/acs.inorgchem.8b02667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The RuIII-based prodrug AziRu efficiently binds to proteins, but the mechanism of its release is still disputed. Herein, in order to test the hypothesis of a reduction-mediated Ru release from proteins, a Raman-assisted crystallographic study on AziRu binding to a model protein (hen egg white lysozyme), in two different oxidation states, RuII and RuIII, was carried out. Our results indicate Ru reduction, but the Ru release upon reduction is dependent on the reducing agent. To better understand this process, a pH-dependent, spectroelectrochemical surface-enhanced Raman scattering (SERS) study was performed also on AziRu-functionalized Au electrodes as a surrogate and simplest model system of RuII- and RuIII-based drugs. This SERS study provided a p Ka of 6.0 ± 0.4 for aquated AziRu in the RuIII state, which falls in the watershed range of pH values separating most cancer environments from their physiological counterparts. These experiments also indicate a dramatic shift of the redox potential E0 by >600 mV of aquated AziRu toward more positive potentials upon acidification, suggesting a selective AziRu reduction in cancer lumen but not in healthy ones. It is expected that the nature of the ligands (e.g., pyridine vs imidazole, present in well-known RuIII complex NAMI-A) will modulate the p Ka and E0, without affecting the underlying reaction mechanism.
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Affiliation(s)
- Marco Caterino
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Mona Herrmann
- Institut für Chemie , Technische Universität Berlin , Straße des 17 Juni 135 , Berlin 10623 , Germany
| | - Antonello Merlino
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Claudia Riccardi
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Maria A Mroginski
- Institut für Chemie , Technische Universität Berlin , Straße des 17 Juni 135 , Berlin 10623 , Germany
| | - Domenica Musumeci
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Francesco Ruffo
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Luigi Paduano
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy
| | - Peter Hildebrandt
- Institut für Chemie , Technische Universität Berlin , Straße des 17 Juni 135 , Berlin 10623 , Germany
| | - Jacek Kozuch
- Institut für Chemie , Technische Universität Berlin , Straße des 17 Juni 135 , Berlin 10623 , Germany
| | - Alessandro Vergara
- Department of Chemical Sciences , University of Naples Federico II , via Cinthia , Naples I-80126 , Italy.,CEINGE, Biotecnologie Avanzate s.c.a.r.l.m. , via G Salvatore , Naples I-80131 , Italy
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10
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Samara YN, Brennan HM, McCarthy L, Bollard MT, Laspina D, Wlodek JM, Campos SL, Natarajan R, Gofron K, McSweeney S, Soares AS, Leroy L. Using sound pulses to solve the crystal-harvesting bottleneck. Acta Crystallogr D Struct Biol 2018; 74:986-999. [PMID: 30289409 PMCID: PMC6173054 DOI: 10.1107/s2059798318011506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 08/14/2018] [Indexed: 01/16/2023] Open
Abstract
Crystal harvesting has proven to be difficult to automate and remains the rate-limiting step for many structure-determination and high-throughput screening projects. This has resulted in crystals being prepared more rapidly than they can be harvested for X-ray data collection. Fourth-generation synchrotrons will support extraordinarily rapid rates of data acquisition, putting further pressure on the crystal-harvesting bottleneck. Here, a simple solution is reported in which crystals can be acoustically harvested from slightly modified MiTeGen In Situ-1 crystallization plates. This technique uses an acoustic pulse to eject each crystal out of its crystallization well, through a short air column and onto a micro-mesh (improving on previous work, which required separately grown crystals to be transferred before harvesting). Crystals can be individually harvested or can be serially combined with a chemical library such as a fragment library.
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Affiliation(s)
- Yasmin N. Samara
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Universidade Federal de Santa Maria, 97105-900 Santa Maria-RS, Brazil
| | - Haley M. Brennan
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biology, College of William and Mary, Williamsburg, VA 23187, USA
| | - Liam McCarthy
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biology, Stony Brook University, New York, NY 11794-5215, USA
| | - Mary T. Bollard
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biology, York College of Pennsylvania, York, PA 17403, USA
| | - Denise Laspina
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biology, Stony Brook University, New York, NY 11794-5215, USA
| | - Jakub M. Wlodek
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Computer Science, Stony Brook University, New York, NY 11794-5215, USA
| | - Stefanie L. Campos
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Clinical Nutrition, Stony Brook University, New York, NY 11794-5215, USA
| | - Ramya Natarajan
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kazimierz Gofron
- Energy Sciences Directorate, NSLS II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Sean McSweeney
- Energy Sciences Directorate, NSLS II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Alexei S. Soares
- Energy Sciences Directorate, NSLS II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Ludmila Leroy
- Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte-MG, Brazil
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11
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Synchrotron Radiation X-ray Diffraction Techniques Applied to Insect Flight Muscle. Int J Mol Sci 2018; 19:ijms19061748. [PMID: 29899245 PMCID: PMC6032142 DOI: 10.3390/ijms19061748] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/04/2018] [Accepted: 06/05/2018] [Indexed: 01/02/2023] Open
Abstract
X-ray fiber diffraction is a powerful tool used for investigating the molecular structure of muscle and its dynamics during contraction. This technique has been successfully applied not only to skeletal and cardiac muscles of vertebrates but also to insect flight muscle. Generally, insect flight muscle has a highly ordered structure and is often capable of high-frequency oscillations. The X-ray diffraction studies on muscle have been accelerated by the advent of 3rd-generation synchrotron radiation facilities, which can generate brilliant and highly oriented X-ray beams. This review focuses on some of the novel experiments done on insect flight muscle by using synchrotron radiation X-rays. These include diffraction recordings from single myofibrils within a flight muscle fiber by using X-ray microbeams and high-speed diffraction recordings from the flight muscle during the wing-beat of live insects. These experiments have provided information about the molecular structure and dynamic function of flight muscle in unprecedented detail. Future directions of X-ray diffraction studies on muscle are also discussed.
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12
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Bury CS, Brooks-Bartlett JC, Walsh SP, Garman EF. Estimate your dose: RADDOSE-3D. Protein Sci 2017; 27:217-228. [PMID: 28921782 DOI: 10.1002/pro.3302] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/10/2017] [Accepted: 09/11/2017] [Indexed: 12/22/2022]
Abstract
We present the current status of RADDOSE-3D, a software tool allowing the estimation of the dose absorbed in a macromolecular crystallography diffraction experiment. The code allows a temporal and spatial dose contour map to be calculated for a crystal of any geometry and size as it is rotated in an X-ray beam, and gives several summary dose values: among them diffraction weighted dose. This allows experimenters to plan data collections which will minimize radiation damage effects by spreading the absorbed dose more homogeneously, and thus to optimize the use of their crystals. It also allows quantitative comparisons between different radiation damage studies, giving a universal "x-axis" against which to plot various metrics.
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Affiliation(s)
- Charles S Bury
- Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | | | - Steven P Walsh
- Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Elspeth F Garman
- Department of Biochemistry, South Parks Road, Oxford, OX1 3QU, United Kingdom
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13
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Safari MS, Byington MC, Conrad JC, Vekilov PG. Polymorphism of Lysozyme Condensates. J Phys Chem B 2017; 121:9091-9101. [DOI: 10.1021/acs.jpcb.7b05425] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mohammad S. Safari
- Department
of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Michael C. Byington
- Department
of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Jacinta C. Conrad
- Department
of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Peter G. Vekilov
- Department
of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
- Department
of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, Texas 77204-5003, United States
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14
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X-ray diffraction measurement of cosolvent accessible volume in rhombohedral insulin crystals. J Struct Biol 2017; 200:213-218. [PMID: 28838818 DOI: 10.1016/j.jsb.2017.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/11/2017] [Accepted: 08/20/2017] [Indexed: 11/21/2022]
Abstract
X-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room temperature and cryo-cooled rhombohedral insulin crystals were equilibrated with 1.2M trehalose to study the effect of lowered water activity. The native and trehalose soaked crystals were isomorphous and had similar structures. Including all the low resolution data, the amplitudes of the structure factors were put on an absolute scale (in units of electrons per asymmetric unit) by constraining the integrated number of electrons inside the envelope of the calculated protein density map to equal the number deduced from the atomic model. This procedure defines the value of F(000), the amplitude at the origin of the Fourier transform, which is equal to the total number of electrons in the asymmetric unit (i.e. protein plus solvent). Comparison of the F(000) values for three isomorphous pairs of room temperature insulin crystals, three with trehalose and three without trehalose, indicates that 75±12 electrons per asymmetric unit were added to the crystal solvent when soaked in 1.2M trehalose. If all the water in the crystal were available as solvent for the trehalose, 304 electrons would have been added. Thus, the co-solvent accessible volume is one quarter of the total water in the crystal. Determination of the total number of electrons in a protein crystal is an essential first step for mapping the average density distribution of the disordered solvent.
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15
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Garman EF, Weik M. X-ray radiation damage to biological macromolecules: further insights. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:1-6. [PMID: 28009541 DOI: 10.1107/s160057751602018x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Despite significant progress made over more than 15 years of research, structural biologists are still grappling with the issue of radiation damage suffered by macromolecular crystals which is induced by the resultant radiation chemistry occurring during X-ray diffraction experiments. Further insights into these effects and the possible mitigation strategies for use in both diffraction and SAXS experiments are given in eight papers in this volume. In particular, damage during experimental phasing is addressed, scavengers for SAXS experiments are investigated, microcrystals are imaged, data collection strategies are optimized, specific damage to tyrosine residues is reexamined, and room temperature conformational heterogeneity as a function of dose is explored. The brief summary below puts these papers into perspective relative to other ongoing radiation damage research on macromolecules.
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Affiliation(s)
- Elspeth F Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Martin Weik
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
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